Commit 6090fa33 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fixed call to sub pipeline

parent bbc21279
......@@ -231,7 +231,7 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
if (filename.endsWith(".gzip")) filename = filename.substring(0,filename.size - 5)
if (filename.endsWith(".fastq")) filename = filename.substring(0,filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
fastqcCommand.output = outDir + "/" + filename + "_fastqc.ouput"
fastqcCommand.output = outDir + "/" + filename + "_fastqc.output"
fastqcCommand.afterGraph
add(fastqcCommand)
return fastqcCommand
......
......@@ -109,7 +109,8 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.outputDir = outputDir + "flexiprep/"
flexiprep.script
flexiprep.init
flexiprep.biopetScript
addAll(flexiprep.functions) // Add function of flexiprep to curent function pool
fastq_R1 = flexiprep.outputFiles("output_R1")
if (paired) fastq_R2 = flexiprep.outputFiles("output_R2")
......
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